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From Chase Master <chasemast...@gmail.com>
Subject Re: Assertion module
Date Mon, 19 Aug 2013 21:18:53 GMT
Thanks for your responses!  Yes, I meant modifying ATTR_SUBJECT to
something more specific like the example you gave.



On Thu, Aug 15, 2013 at 10:51 AM, Chen, Pei
<Pei.Chen@childrens.harvard.edu>wrote:

> > ATTR_SUBJECT_ in edu.mayo.bmi.uima.core.type.constants.CONST, is it
> > possible to meaningfully change them?
> Could you clarify a bit more about meaningfully changing them?  i.e. did
> you mean to write another classifier to make the subject attribute more
> specific? Such as "sibling, biological father/mother?"
> I presume you mean ATTR_SUBJECT* in:
>
> http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-type-system/src/main/java/org/apache/ctakes/typesystem/type/constants/CONST.java
>
> You may find the below links helpful:
> ML:
> http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngine.java
> And additional Rules:
> http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/SubjectAttributeAnalysisEngine.java
>
> > -----Original Message-----
> > From: Wu, Stephen T., Ph.D. [mailto:Wu.Stephen@mayo.edu]
> > Sent: Thursday, August 15, 2013 11:49 AM
> > To: dev@ctakes.apache.org
> > Subject: Re: Assertion module
> >
> > Hi chase,
> >
> > >pipeline, which calls the Assertion module.  I noticed that for
> > >something like ³Anna¹s father has had knee pain for years², the subject
> > >attribute gets set to family_member.  Is it possible to be more
> specific?
> > See below.
> >
> > >
> > >does it assume that the subject of every statement is the patient
> > >unless the phrase suggests otherwise?
> > Yes.
> >
> > >If the possible values are specified by the prefix ATTR_SUBJECT_ in
> > >edu.mayo.bmi.uima.core.type.constants.CONST, is it possible to
> > >meaningfully change them?
> > CONST does indeed include all the possible values.  It is possible to
> rewrite
> > the Subject annotator in the assertion module such that other values can
> be
> > assigned.  However, you would be working without "meaningful" evaluation
> > on its accuracy.  In other words, if you assign "family_member" we have
> > human-annotated cases of what that looks like, but if we come up with a
> > new method to assign "father" we have no way to figure out whether we're
> > doing a good job or not.
> >
> > >Also, the value of ³confidence² is set by the assertion module.  Is the
> > >score referencing the assignment of subject, or whether it¹s generic,
> > >or the polarity, or other attributes?
> > I believe the "confidence" number was intended to be for the named entity
> > recognition (ctakes-dictionary-lookup). The newer version of assertion
> (in
> > trunk but not the default in ctakes-clinical-pipeline) does not assign
> this
> > value.  Matt Coarr -- any comments on what the medfacts version does?
> >
> > hth
> >
> > stephen
>
>

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